Next generation sequencing (NGS/HTS) tools.
###Using ngs
Artifacts from this project are available from the Maven Central repository.
E.g.
<dependency>
<groupId>org.nmdp.ngs</groupId>
<artifactId>ngs-align</artifactId>
<version>${version}</version>
</dependency>###Using ngs-tools
The ngs-tools module builds several command line tools.
For example
$ ngs-downsample-fastq -h
usage:
ngs-downsample-fastq -p 0.5 [args]
arguments:
-a, --about display about message [optional]
-h, --help display help message [optional]
-i, --input-fastq-file [class java.io.File] input FASTQ file, default stdin [optional]
-o, --output-fastq-file [class java.io.File] output FASTQ file, default stdout [optional]
-p, --probability [class java.lang.Double] probability a FASTQ record will be removed, [0.0-1.0] [required]
-z, --seed [class java.lang.Integer] random number seed, default relates to current time [optional]###Hacking ngs
Install
- JDK 1.7 or later, http://openjdk.java.net
- Apache Maven 3.2.5 or later, http://maven.apache.org
To build
$ mvn install